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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagagatctttactcttaatttcttcgtaccaattatctaaagtaaatagaaccttctgtccttttcatatcattaaattttatcggtattttgaaacagGTCCTGAGCATGAGTAGACTGGGTGGAGCTGGTGCTGTTGCTCAGCTTGTGGCTGATGTTCCCCTTTCTGCAGTGGAG

Basic information

species Glycine max
transcript GLYMA20G36770.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36770.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g58330.1 (Oryza sativa), 3'ss of exon 5
aagagatctttactcttaatttcttcgtaccaattatcta--aagtaaatagaaccttctgtccttttcatatcattaaattttatcggtattttgaaacagGTCCTGAGCATGAGTAGACTGGGTGGAGCTGGTGCTGTTGCTCAGCTTGTGGCTGATGTTCCCCTTTCTGCAGTGGAG
               ||   |||    | | | |||||||  ||| | | |  || || |||  ||||  |    | | |    ||   | | | |    ||||  | |||||||| || |||||||| || ||||||||||| ||||| || |||||| |||| ||||| |    |   
--------------gtttggttcactatgcta-ttatctagtaagcataaaccacattttgtgtttttagttgtttgatagagcatgattctatggtggtagGTTTTAAGCATGAGCAGGCTGGGTGGCGCGGGTGCTGTTGCACAGCTGGTTGCTGATATTCCACTTTCAGTTAAG---

upper sequence: GLYMA20G36770.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0030g02230.t01 (Vitis vinifera), 3'ss of exon 5
aagagatctttactcttaatttcttcgtac-caattatc-taaagtaaatagaaccttctgtccttttcatatcattaaatttt-atcggtattttgaaacagGTCCTGAGCATGAGTAGACTGGGTGGAGCTGGTGCTGTTGCTCAGCTTGTGGCTGATGTTCCCCTTTCTGCAGTGGAG
     | |  || |  ||    |  |  |  || ||||  |    | | | | |  ||   |  || ||||||   |||||||| || | |   || ||||||||  |||||||||| ||||| |||||||| ||||| || || ||||| || |||||||||||| | |   || | |||
---caaacggtaatgctatcaccaccacattcacttatagtgcttttatttgcatttttatttgttgtcatatttataaattttcattgttgaatttaaacagGTTTTGAGCATGAGCAGACTTGGTGGAGCAGGTGCAGTAGCCCAGCTGGTAGCTGATGTTCCCTTGTTATCAATTGAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|31561061|gb|CD486899.1|CD486899
EST:     GCTTGATGAAATAGTGGACTATGTGAAGTTCCTTAGGCTTCAGGTTAAG                         GTCCTGAGCATGAGTAGACTGGGTGGAGCTGGTGCTGTTGCTCAGCTTGTG
genomic: GCTTGATGAAATTGTGGACTATGTGAAGTTCCTTAGGCTTCAGGTTAAGgtatgaaagc ... tttgaaacagGTCCTGAGCATGAGTAGACTGGGTGGAGCTGGTGCTGTTGCTCAGCTTGTG
EST: gi|31471826|gb|CD413854.1|CD413854
EST:     GCTTGATGAAATTGTGGACTATGTGAAGTTCCTTAGGCTTCAGGTTAAG                         GTCCTGAGCATGAGTAGACTGGGTGGAGCTGGTGCTGTTGCTCAGCTTGTG
genomic: GCTTGATGAAATTGTGGACTATGTGAAGTTCCTTAGGCTTCAGGTTAAGgtatgaaagc ... tttgaaacagGTCCTGAGCATGAGTAGACTGGGTGGAGCTGGTGCTGTTGCTCAGCTTGTG
EST: gi|31305735|gb|CD390938.1|CD390938
EST:     GCTTGATGAAATTGTGGACTATGTGAAGTTCCTTAGGCTTCAGGTTAAG                         GTCCTGAGCATGAGTAGACTGGGTGGAGCTGGTGCTGTTGCTCAGCTTGTG
genomic: GCTTGATGAAATTGTGGACTATGTGAAGTTCCTTAGGCTTCAGGTTAAGgtatgaaagc ... tttgaaacagGTCCTGAGCATGAGTAGACTGGGTGGAGCTGGTGCTGTTGCTCAGCTTGTG
EST: gi|20449248|gb|BQ253372.1|BQ253372
EST:     TGGTTGATGAAATTGTGGACTATGTGAAGTTCCTTAGGCTTTAGGTTTAG                         GTCCTGAGCATGAGTAGACTGGGTGGAGCTGGTGCTGTTGCTCAGCTTGTG
genomic: TGCTTGATGAAATTGTGGACTATGTGAAGTTCCTTAGGCTTCAGGTTAAGgtatgaaagc ... tttgaaacagGTCCTGAGCATGAGTAGACTGGGTGGAGCTGGTGCTGTTGCTCAGCTTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatagaaccttctgtccttttcatatcattaaattttatcggtattttgaaacagGTCCTGAGCATGAGTAGACTGGGTGGAGCTGGTGCTGTTGCTCAGCTTGTGGCTGATGTTCCCCTTTCTGCAGTGGAG
                 ttttcatatcattaaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagagatctttactcttaatttcttcgtaccaattatctaaagtaaatagaaccttctgtccttttcatatcattaaattttatcggtattttgaaacagGTCCTGAGCATGAGTAGACTGGGTGGAGCTGGTGCTGTTGCTCAGCTTGTGGCTGATGTTCCCCTTTCTGCAGTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - aaatagaa